Merge pull request #26 from andyquinterom/syms

Adds NodeVec and Symbols

Author: andyquinterom

.Rbuildignore

@@ -29,3 +29,6 @@
 ^src/rust/\.cargo$
 ^src/orbweaver\.so$
 ^Makefile
+
+^benchmarks/
+^assets/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: orbweaver
 Title: Fast and Efficient Graph Data Structures
-Version: 0.11.0
+Version: 0.12.0
 Authors@R: 
     c(person(given = "ixpantia, SRL",
              role = "cph",

NAMESPACE

@@ -3,9 +3,12 @@
 S3method("$",DirectedAcyclicGraph)
 S3method("$",DirectedGraph)
 S3method("$",DirectedGraphBuilder)
+S3method("$",NodeVec)
 S3method("[[",DirectedAcyclicGraph)
 S3method("[[",DirectedGraph)
 S3method("[[",DirectedGraphBuilder)
+S3method("[[",NodeVec)
+S3method(as.character,NodeVec)
 S3method(children,DirectedAcyclicGraph)
 S3method(children,DirectedGraph)
 S3method(find_all_paths,DirectedAcyclicGraph)
@@ -29,10 +32,12 @@ S3method(least_common_parents,DirectedGraph)
 S3method(length,DirectedAcyclicGraph)
 S3method(length,DirectedGraph)
 S3method(length,DirectedGraphBuilder)
+S3method(length,NodeVec)
 S3method(parents,DirectedAcyclicGraph)
 S3method(parents,DirectedGraph)
 S3method(print,DirectedAcyclicGraph)
 S3method(print,DirectedGraph)
+S3method(print,NodeVec)
 S3method(subset,DirectedAcyclicGraph)
 S3method(subset,DirectedGraph)
 export(add_edge)

R/extendr-wrappers.R

@@ -122,5 +122,19 @@ DirectedGraphBuilder$build_acyclic <- function() .Call(wrap__DirectedGraphBuilde
 #' @export
 `[[.DirectedGraphBuilder` <- `$.DirectedGraphBuilder`
 
+NodeVec <- new.env(parent = emptyenv())
+
+NodeVec$print <- function() invisible(.Call(wrap__NodeVec__print, self))
+
+NodeVec$as_character <- function() .Call(wrap__NodeVec__as_character, self)
+
+NodeVec$len <- function() .Call(wrap__NodeVec__len, self)
+
+#' @export
+`$.NodeVec` <- function (self, name) { func <- NodeVec[[name]]; environment(func) <- environment(); func }
+
+#' @export
+`[[.NodeVec` <- `$.NodeVec`
+
 
 # nolint end

R/nodevec.R

@@ -0,0 +1,14 @@
+#' @export
+print.NodeVec <- function(x, ...) {
+  x$print()
+}
+
+#' @export
+as.character.NodeVec <- function(x, ...) {
+  x$as_character()
+}
+
+#' @export
+length.NodeVec <- function(x, ...) {
+  x$len()
+}

README.md

@@ -8,18 +8,27 @@
 
 ## Overview
 
-A fast R library for working with Nodes in a graph. This library
-modifies graphs in place, similar to how [data.table](https://github.com/Rdatatable/data.table)
-modifies data.frames in place. This allows for fast and memory efficient
-graph operations.
+A fast R library for working with Nodes in a graph.
 
 ## Features
 
- - Nodes can store arbitrary data
+ - Find shortest paths between nodes in a graph
  - Find the common parents between selected nodes
- - Modify graphs in place
  - Directed Graph
  - Directed Acyclic Graph
+ - It is quite fast
+
+## Why not igraph?
+
+[igraph](https://igraph.org/) is an amazing network analysis package.
+igraph is much more mature and orbweaver focuses on extreme performance
+and low latency operations. If you need super high performance
+and do not require weighted graphs, orbweaver may be for you.
+
+![igraph vs orbweaver benchmark](assets/benchmark.png)
+
+> We may add weighted graph in the future but for not
+> it is not in the short-term road map.
 
 ## Installation
 

assets/benchmark.png

@@ -0,0 +1,99 @@
+library(igraph)
+library(orbweaver)
+library(microbenchmark)
+
+# Download the dataset from the orbweaver-rs repo
+edges <- readr::read_tsv("https://raw.githubusercontent.com/ixpantia/orbweaver-rs/main/assets/medium.txt", col_names = c("parent", "child"))
+
+# Function to convert dataframe to orbweaver graph
+df_to_orbweaver <- function(edges) {
+  graph_builder() |>
+    populate_edges(edges, parent, child) |>
+    build_acyclic()
+}
+
+# Function to convert dataframe to igraph graph
+df_to_igraph <- function(edges) {
+  graph_from_data_frame(edges, directed = TRUE)
+}
+
+find_paths_orbweaver <- function(graph, from, to) {
+  orbweaver::find_all_paths(graph, from, to)
+}
+
+find_paths_igraph <- function(graph, from, to) {
+  igraph::all_shortest_paths(graph, from, to)
+}
+
+find_path_orbweaver <- function(graph, from, to) {
+  orbweaver::find_path(graph, from, to)
+}
+
+find_path_igraph <- function(graph, from, to) {
+  igraph::shortest_paths(graph, from, to)$vpath
+}
+
+get_nodes_orbweaver <- function(graph) {
+  orbweaver::nodes(graph)
+}
+
+get_nodes_igraph <- function(graph) {
+  igraph::V(graph)
+}
+
+get_leaves_under_orbweaver <- function(graph, node) {
+  orbweaver::get_leaves_under(graph, node)
+}
+
+get_leaves_under_igraph <- function(graph, node) {
+  descendants <- igraph::ego(graph, order = length(V(graph)), nodes = node, mode = "out")[[1]]
+  descendants[igraph::degree(graph, v = descendants, mode = "out") == 0]
+}
+
+get_roots_over_orbweaver <- function(graph, node) {
+  orbweaver::get_roots_over(graph, node)
+}
+
+get_roots_over_igraph <- function(graph, node) {
+  ancestors <- igraph::ego(graph, order = length(V(graph)), nodes = node, mode = "in")[[1]]
+  ancestors[igraph::degree(graph, v = ancestors, mode = "in") == 0]
+}
+
+least_common_parents_orbweaver <- function(graph, nodes) {
+  orbweaver::least_common_parents(graph, nodes)
+}
+
+least_common_parents_igraph <- function(graph, nodes) {
+  subgraph <- igraph::induced_subgraph(graph, nodes)
+  igraph::V(subgraph)[igraph::degree(subgraph, mode = "in") == 0]
+}
+
+subset_orbweaver <- function(graph, node) {
+  subset(graph, node)
+}
+
+subset_igraph <- function(graph, node) {
+  reachable_nodes <- igraph::ego(graph, order = length(igraph::V(graph)), nodes = node, mode = "out")[[1]]
+  igraph::induced_subgraph(graph, reachable_nodes)
+}
+
+# Create orbweaver and igraph graphs
+g_orb <- df_to_orbweaver(edges)
+g_ig <- df_to_igraph(edges)
+
+# Benchmark the functions
+microbenchmark(
+  find_all_paths_orbweaver = find_paths_orbweaver(g_orb, "1781f676dedf5767f3243db0a9738b35", "eb85851afd251bd7c7eaf725d0d19360"),
+  find_all_paths_igraph = find_paths_igraph(g_ig, "1781f676dedf5767f3243db0a9738b35", "eb85851afd251bd7c7eaf725d0d19360"),
+  find_path_orbweaver = find_path_orbweaver(g_orb, "1781f676dedf5767f3243db0a9738b35", "eb85851afd251bd7c7eaf725d0d19360"),
+  find_path_igraph = find_path_igraph(g_ig, "1781f676dedf5767f3243db0a9738b35", "eb85851afd251bd7c7eaf725d0d19360"),
+  get_leaves_under_orbweaver = get_leaves_under_orbweaver(g_orb, "1781f676dedf5767f3243db0a9738b35"),
+  get_leaves_under_igraph = get_leaves_under_igraph(g_ig, "1781f676dedf5767f3243db0a9738b35"),
+  get_roots_over_orbweaver = get_roots_over_orbweaver(g_orb, "eb85851afd251bd7c7eaf725d0d19360"),
+  get_roots_over_igraph = get_roots_over_igraph(g_ig, "eb85851afd251bd7c7eaf725d0d19360"),
+  least_common_parents_orbweaver = least_common_parents_orbweaver(g_orb, edges$parent[1:100]),
+  least_common_parents_igraph = least_common_parents_igraph(g_ig, edges$parent[1:100]),
+  subset_orbweaver = subset_orbweaver(g_orb, "1781f676dedf5767f3243db0a9738b35"),
+  subset_igraph = subset_igraph(g_ig, "1781f676dedf5767f3243db0a9738b35"),
+  times = 100
+)

benchmarks/bench.R

@@ -10,7 +10,8 @@ name = 'orbweaver'
 [dependencies]
 # extendr-api = { version = "0.6", features = ["serde"] }
 extendr-api = { git = "https://github.com/extendr/extendr.git", rev = "cb85a21a90c3fcb538a40fcea03058454edb3dac" }
-orbweaver = { version = "0.11.0" }
+orbweaver = { version = "0.12.0" }
+#orbweaver = { git = "https://github.com/ixpantia/orbweaver-rs.git", branch = "main" }
 
 # This will help us filter the platforms
 # we support to make the final bundle size